[gmx-users] How to solve the "LINCS WARNING" problem

[변진영]

Hi Yu

I simulated the both case (1), (2) for only all-atom ligand system and only protein system respectively you mentioned.
I run the each case; the NVT and NPT equilibration with 200ps and 1ns respectively. And there are no problems during NVT and NPT equilibration.

And while I wrote the ligand only topology file, I realized that there is specific order in writing topology file (before I don’t exactly know about the order.)

Below is the last section of  my topology file:

 ; Include Position restraint file
#ifdef POSRES
#include "../PROTEIN/posre.itp"
#endif

#include "../LIGAND/lig.itp"

#ifdef POSRES_LIG
#include "../LIGAND/lig_posre.itp"
#endif


; Include water topology
#include "gromos54a7_atb_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "gromos54a7_atb_lipid.ff/ions.itp"

[ system ]
; Name
--- in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
LIG                 1
SOL         30059
NA               4

—————————————————————————————————————

Is there any problem with my topology file and Is it the right order?

Thank you very much b, You

> 2020. 4. 17. 오후 3:34, Yu Du <ydu-sci at outlook.com> 작성:
> 
> Hi Jinyoung,
> 
> You made it clear.
> 
> If you do not have special needs in all-atom version of the ligand, you can also try the united-atom topology of the very same ligand.
> 
> To check the origin of LINCS WARNING, I suggest running MD simulation with only protein and only ligand in the same process you followed in a divide and conquer strategy.
> 
> Could you run the following simulation to pinpoint the error?
> 
> (1) Simulation only all-atom ligand in the system.
> (2) Simulation only protein in the system.
> (3) Simulation only united-atom ligand in the system if it's possible.
> 
> In the end, I noticed that you used ATB topology, so you need to strictly follow the instruction in the ATB ff file folders for protein-ligand simulation.
> 
> PS: gmx-users mail list do not receive attachment.
> 
> Cheers,
> Yu
> 
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